Please perform the following steps:
1. Make sure that you are using a predefined template (without changes) shipped with installation of Entity Developer: disable current template (right click on it > Disable), then right click on the Templates node in Model Explorer > New Template > DbContext > OK.
2. Specify all non-default properties of the used DbContext template.
3. Tell us your current version (x.x.xxx) of Entity Developer.
4. Send us a test model to reproduce the issue with incorrect code generation.